Correlogram using GGally Package

Scatterplot matrix using ggpairs()

# library("GGally")
 
# Create data 
data <- data.frame( var1 = 1:100 + rnorm(100,sd=20), 
                    v2 = 1:100 + rnorm(100,sd=27), 
                    v3 = rep(1, 100) + rnorm(100, sd = 1)) 
data$v4 = data$var1 ** 2 
data$v5 = -(data$var1 ** 2) 
 
# Check correlations (as scatterplots), distribution and print corrleation coefficient 
ggpairs(data, title="correlogram with ggpairs()") 

## Split by group
data(flea)
ggpairs(flea, columns = 2:4, ggplot2::aes(colour=species))

Visualize correlation using ggcorr()

# library("GGally")
 
# Create data 
data <- data.frame( var1 = 1:100 + rnorm(100,sd=20), 
                    v2 = 1:100 + rnorm(100,sd=27), 
                    v3 = rep(1, 100) + rnorm(100, sd = 1)) 
data$v4 = data$var1 ** 2 
data$v5 = -(data$var1 ** 2) 
 
# Check correlation between variables
#cor(data) 
 
# Nice visualization of correlations
ggcorr(data, method = c("everything", "pearson"))

Change plot types

# From the help page:
data(tips, package = "reshape")
ggpairs(
  tips[, c(1, 3, 4, 2)],
  upper = list(continuous = "density", combo = "box_no_facet"),
  lower = list(continuous = "points", combo = "dot_no_facet")
)

Correlogram using corrgram Package

Scatterplot matrix with ggpairs()

Relationship can be visualized with different methods:

  • panel.ellipse to display ellipses
  • panel.shade for coloured squares
  • panel.pie for pie charts
  • panel.pts for scatterplots
# Corrgram library
# library("corrgram")

# mtcars dataset is natively available in R
# head(mtcars)

# First
corrgram(mtcars, 
         order=TRUE, 
         lower.panel=panel.shade, 
         upper.panel=panel.pie, 
         text.panel=panel.txt, 
         main="Car Milage Data in PC2/PC1 Order") 

# Second
corrgram(mtcars, 
         order=TRUE, 
         lower.panel=panel.ellipse, 
         upper.panel=panel.pts, 
         text.panel=panel.txt, 
         diag.panel=panel.minmax, 
         main="Car Milage Data in PC2/PC1 Order") 

# Third
corrgram(mtcars, 
         order=NULL, 
         lower.panel=panel.shade, 
         upper.panel=NULL, 
         text.panel=panel.txt, 
         main="Car Milage Data (unsorted)")

Interactive trellis plot (plotly Package)

# library(plotly)

adsl <- read_xpt("./01_Datasets/adsl.xpt")

pl_colorscale=list(c(0.0, '#19d3f3'),
                   c(0.333, '#19d3f3'),
                   c(0.333, '#e763fa'),
                   c(0.666, '#e763fa'),
                   c(0.666, '#636efa'),
                   c(1, '#636efa'))

fig <- adsl %>%
  plot_ly() 
fig <- fig %>%
  add_trace(
    type = 'splom',
    dimensions = list(
      list(label='Age', values=~AGE),
      list(label='Height', values=~HEIGHTBL),
      list(label='Weight', values=~WEIGHTBL),
      list(label='BMI', values=~BMIBL)
    ),
    text=~TRT01P,
    marker = list(
      color = as.integer(adsl$TRT01PN),
      colorscale = pl_colorscale,
      size = 7,
      line = list(
        width = 1,
        color = 'rgb(230,230,230)'
      )
    )
  ) 

fig <- fig %>%
  layout(
    title= 'ADSL Data set',
    plot_bgcolor='rgba(240,240,240, 0.95)'
  )

fig2 <-  fig %>% style(diagonal = list(visible = F))
fig2
# htmlwidgets::saveWidget(as_widget(fig2), "./02_Plots/Visualization/WW Dec2023b.html")

GGally Package

# library(GGally)

adsl <- read_xpt("./01_Datasets/adsl.xpt")
adsl_data <- adsl[, c("AGE", "BMIBL", "HEIGHTBL", "WEIGHTBL","SEX")]


# Convert SEX to a factor if it’s not already
adsl_data$SEX <- as.factor(adsl_data$SEX)

# Create a pair plot with grouping by SEX
ggpairs(
  adsl_data,
  aes(color = SEX, fill = SEX),  # Color by SEX
  lower = list(continuous = wrap("smooth", alpha = 0.3, size = 0.5)),
  diag = list(continuous = wrap("densityDiag")),
  upper = list(continuous = wrap("cor", size = 4, color = "black"))
) +
  theme_minimal() +
  theme(
    strip.text = element_text(size = 10),
    axis.text = element_text(size = 8)
  ) +
  scale_fill_manual(values = c("pink", "lightblue")) +  # Customize colors if desired
  scale_color_manual(values = c("pink", "lightblue"))